Antigen-specific T lymphocyte activation occurs through the clonally distributed T cell receptor (TCR), which is involved in thymocyte selection and peripheral T cell effector responses. How TCR-dependent lineage commitment from a common precursor occurs for the two major subsets of T cells, the CD4+ and CD8+ cells, remains unknown. Furthermore, the quantitative and qualitative relationships between receptor occupancy and signaling for differentiation are also poorly understood. This project uses cellular, biochemical, and molecular approaches to study differentiation of thymocytes and activation of T cells upon ligand engagement. Our previous studies suggested that thymocyte development could involve lineage choice and partial maturation that is independent of the MHC class involved in T cell recognition, followed by complete maturation (positive selection) of those cells whose remaining expression of CD4 or CD8 matched the MHC class-specificity of the T cell receptor. Studies of gene targeted and chimeric mice support this conclusion and show that recognition of thymic epithelial MHC per se is critical to the first step in development. Characterization of mature and transitional phenotype cells in invariant chain-deficient mice has also allowed new insights into the quantitative parameters of thymocyte deletion. We previously reported that some TCR ligands evoke only a subset of T cell effector responses, and that such variant ligands can selectively antagonize cytokine production induced by receptor agonists. New studies show that variant ligands induce only a subset of the tyrosine phosphorylation events typically accompanying agonist recognition. These variant signal transduction events indirectly affect biological responses such an anergy, and can arise not only from changes in the TCR ligand, but also alterations in the signaling machinery of the T cell. Along with our work on the molecular organization of T cell signal transduction complexes (Z01 AI 00349-12 LI), this helps explain how protein-protein interactions result in antigen receptor-dependent second messenger generation, and how specific intracellular signals contribute to the downstream gene activation events in T cells that control effector function and tolerance induction.